data_3ZD4 # _entry.id 3ZD4 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.384 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3ZD4 pdb_00003zd4 10.2210/pdb3zd4/pdb PDBE EBI-54902 ? ? WWPDB D_1290054902 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2012-12-12 2 'Structure model' 1 1 2013-03-06 3 'Structure model' 1 2 2014-09-10 4 'Structure model' 1 3 2014-09-17 5 'Structure model' 2 0 2022-11-02 6 'Structure model' 2 1 2024-01-31 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' Other 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Database references' 4 5 'Structure model' 'Atomic model' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 5 'Structure model' Other 8 5 'Structure model' 'Source and taxonomy' 9 6 'Structure model' 'Data collection' 10 6 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 5 'Structure model' atom_site 2 5 'Structure model' atom_site_anisotrop 3 5 'Structure model' database_2 4 5 'Structure model' pdbx_database_status 5 5 'Structure model' pdbx_entity_src_syn 6 5 'Structure model' struct_conn 7 5 'Structure model' struct_ref 8 6 'Structure model' chem_comp_atom 9 6 'Structure model' chem_comp_bond 10 6 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_atom_site.B_iso_or_equiv' 2 5 'Structure model' '_atom_site.Cartn_x' 3 5 'Structure model' '_atom_site.Cartn_y' 4 5 'Structure model' '_atom_site.Cartn_z' 5 5 'Structure model' '_atom_site.auth_atom_id' 6 5 'Structure model' '_atom_site.label_atom_id' 7 5 'Structure model' '_atom_site.type_symbol' 8 5 'Structure model' '_atom_site_anisotrop.U[1][1]' 9 5 'Structure model' '_atom_site_anisotrop.U[1][2]' 10 5 'Structure model' '_atom_site_anisotrop.U[1][3]' 11 5 'Structure model' '_atom_site_anisotrop.U[2][2]' 12 5 'Structure model' '_atom_site_anisotrop.U[2][3]' 13 5 'Structure model' '_atom_site_anisotrop.U[3][3]' 14 5 'Structure model' '_atom_site_anisotrop.pdbx_auth_atom_id' 15 5 'Structure model' '_atom_site_anisotrop.pdbx_label_atom_id' 16 5 'Structure model' '_atom_site_anisotrop.type_symbol' 17 5 'Structure model' '_database_2.pdbx_DOI' 18 5 'Structure model' '_database_2.pdbx_database_accession' 19 5 'Structure model' '_pdbx_database_status.status_code_sf' 20 5 'Structure model' '_pdbx_entity_src_syn.pdbx_beg_seq_num' 21 5 'Structure model' '_pdbx_entity_src_syn.pdbx_end_seq_num' 22 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 23 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 24 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 25 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 26 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 27 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 28 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 29 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 30 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 31 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 32 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 33 5 'Structure model' '_struct_ref.pdbx_align_begin' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3ZD4 _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2012-11-24 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 3ZP8 unspecified 'HIGH-RESOLUTION FULL-LENGTH HAMMERHEAD RIBOZYME' PDB 3ZD5 unspecified 'THE 2.2 A STRUCTURE OF A FULL-LENGTH CATALYTICALLY ACTIVE HAMMERHEAD RIBOZYME' # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Scott, W.G.' 1 'Schultz, E.' 2 # _citation.id primary _citation.title ;Structural and Catalytic Effects of an Invariant Purine Substitution in the Hammerhead Ribozyme: Implications for the Mechanism of Acid-Base Catalysis. ; _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 70 _citation.page_first 2256 _citation.page_last ? _citation.year 2014 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 25195740 _citation.pdbx_database_id_DOI 10.1107/S1399004714010608 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Schultz, E.P.' 1 ? primary 'Vasquez, E.E.' 2 ? primary 'Scott, W.G.' 3 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'HAMMERHEAD RIBOZYME, ENZYME STRAND' 13925.326 1 ? ? ? ? 2 polymer syn 'HAMMERHEAD RIBOZYME, SUBSTRATE STRAND' 6333.816 1 ? ? ? ? 3 water nat water 18.015 31 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no yes '(GDP)GAUGUACUACCAGCUGAUGAGUCCCAAAUAGGACAAAACGCC' GGAUGUACUACCAGCUGAUGAGUCCCAAAUAGGACAAAACGCC A ? 2 polyribonucleotide no yes 'GGCGU(OMC)CUGGUAUCCAAUC(DC)' GGCGUCCUGGUAUCCAAUCC B ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GDP n 1 2 G n 1 3 A n 1 4 U n 1 5 G n 1 6 U n 1 7 A n 1 8 C n 1 9 U n 1 10 A n 1 11 C n 1 12 C n 1 13 A n 1 14 G n 1 15 C n 1 16 U n 1 17 G n 1 18 A n 1 19 U n 1 20 G n 1 21 A n 1 22 G n 1 23 U n 1 24 C n 1 25 C n 1 26 C n 1 27 A n 1 28 A n 1 29 A n 1 30 U n 1 31 A n 1 32 G n 1 33 G n 1 34 A n 1 35 C n 1 36 A n 1 37 A n 1 38 A n 1 39 A n 1 40 C n 1 41 G n 1 42 C n 1 43 C n 2 1 G n 2 2 G n 2 3 C n 2 4 G n 2 5 U n 2 6 OMC n 2 7 C n 2 8 U n 2 9 G n 2 10 G n 2 11 U n 2 12 A n 2 13 U n 2 14 C n 2 15 C n 2 16 A n 2 17 A n 2 18 U n 2 19 C n 2 20 DC n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample 1 43 'SYNTHETIC CONSTRUCT' ? 32630 ? 2 1 sample 1 20 'SYNTHETIC CONSTRUCT' ? 32630 ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 GDP 'RNA linking' n "GUANOSINE-5'-DIPHOSPHATE" ? 'C10 H15 N5 O11 P2' 443.201 HOH non-polymer . WATER ? 'H2 O' 18.015 OMC 'RNA linking' n "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O8 P' 337.223 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GDP 1 1 1 GDP GDP A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 U 4 4 4 U U A . n A 1 5 G 5 5 5 G G A . n A 1 6 U 6 6 6 U U A . n A 1 7 A 7 7 7 A A A . n A 1 8 C 8 8 8 C C A . n A 1 9 U 9 9 9 U U A . n A 1 10 A 10 10 10 A A A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n A 1 13 A 13 13 13 A A A . n A 1 14 G 14 14 14 G G A . n A 1 15 C 15 15 15 C C A . n A 1 16 U 16 16 16 U U A . n A 1 17 G 17 17 17 G G A . n A 1 18 A 18 18 18 A A A . n A 1 19 U 19 19 19 U U A . n A 1 20 G 20 20 20 G G A . n A 1 21 A 21 21 21 A A A . n A 1 22 G 22 22 22 G G A . n A 1 23 U 23 23 23 U U A . n A 1 24 C 24 24 24 C C A . n A 1 25 C 25 25 25 C C A . n A 1 26 C 26 26 26 C C A . n A 1 27 A 27 27 27 A A A . n A 1 28 A 28 28 28 A A A . n A 1 29 A 29 29 29 A A A . n A 1 30 U 30 30 30 U U A . n A 1 31 A 31 31 31 A A A . n A 1 32 G 32 32 32 G G A . n A 1 33 G 33 33 33 G G A . n A 1 34 A 34 34 34 A A A . n A 1 35 C 35 35 35 C C A . n A 1 36 A 36 36 36 A A A . n A 1 37 A 37 37 37 A A A . n A 1 38 A 38 38 38 A A A . n A 1 39 A 39 39 39 A A A . n A 1 40 C 40 40 40 C C A . n A 1 41 G 41 41 41 G G A . n A 1 42 C 42 42 42 C C A . n A 1 43 C 43 43 43 C C A . n B 2 1 G 1 1 1 G G B . n B 2 2 G 2 2 2 G G B . n B 2 3 C 3 3 3 C C B . n B 2 4 G 4 4 4 G G B . n B 2 5 U 5 5 5 U U B . n B 2 6 OMC 6 6 6 OMC OMC B . n B 2 7 C 7 7 7 C C B . n B 2 8 U 8 8 8 U U B . n B 2 9 G 9 9 9 G G B . n B 2 10 G 10 10 10 G G B . n B 2 11 U 11 11 11 U U B . n B 2 12 A 12 12 12 A A B . n B 2 13 U 13 13 13 U U B . n B 2 14 C 14 14 14 C C B . n B 2 15 C 15 15 15 C C B . n B 2 16 A 16 16 16 A A B . n B 2 17 A 17 17 17 A A B . n B 2 18 U 18 18 18 U U B . n B 2 19 C 19 19 19 C C B . n B 2 20 DC 20 20 20 DC DC B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 HOH 1 2001 2001 HOH HOH A . C 3 HOH 2 2002 2002 HOH HOH A . C 3 HOH 3 2003 2003 HOH HOH A . C 3 HOH 4 2004 2004 HOH HOH A . C 3 HOH 5 2005 2005 HOH HOH A . C 3 HOH 6 2006 2006 HOH HOH A . C 3 HOH 7 2007 2007 HOH HOH A . C 3 HOH 8 2008 2008 HOH HOH A . C 3 HOH 9 2009 2009 HOH HOH A . C 3 HOH 10 2010 2010 HOH HOH A . C 3 HOH 11 2011 2011 HOH HOH A . C 3 HOH 12 2012 2012 HOH HOH A . C 3 HOH 13 2013 2013 HOH HOH A . C 3 HOH 14 2014 2014 HOH HOH A . C 3 HOH 15 2015 2015 HOH HOH A . C 3 HOH 16 2016 2016 HOH HOH A . C 3 HOH 17 2017 2017 HOH HOH A . C 3 HOH 18 2018 2018 HOH HOH A . C 3 HOH 19 2019 2019 HOH HOH A . C 3 HOH 20 2020 2020 HOH HOH A . C 3 HOH 21 2021 2021 HOH HOH A . D 3 HOH 1 2001 2001 HOH HOH B . D 3 HOH 2 2002 2002 HOH HOH B . D 3 HOH 3 2003 2003 HOH HOH B . D 3 HOH 4 2004 2004 HOH HOH B . D 3 HOH 5 2005 2005 HOH HOH B . D 3 HOH 6 2006 2006 HOH HOH B . D 3 HOH 7 2007 2007 HOH HOH B . D 3 HOH 8 2008 2008 HOH HOH B . D 3 HOH 9 2009 2009 HOH HOH B . D 3 HOH 10 2010 2010 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal PHENIX refinement '(PHENIX.REFINE)' ? 1 iMOSFLM 'data reduction' . ? 2 SCALA 'data scaling' . ? 3 PHASER phasing . ? 4 # _cell.entry_id 3ZD4 _cell.length_a 50.140 _cell.length_b 68.450 _cell.length_c 60.220 _cell.angle_alpha 90.00 _cell.angle_beta 112.56 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ZD4 _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 # _exptl.entry_id 3ZD4 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.35 _exptl_crystal.density_percent_sol 47.74 _exptl_crystal.description 'G12A MUTATED AND MODELED IN COOT' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.097173 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SSRL BEAMLINE BL7-1' _diffrn_source.pdbx_synchrotron_site SSRL _diffrn_source.pdbx_synchrotron_beamline BL7-1 _diffrn_source.pdbx_wavelength 1.097173 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 3ZD4 _reflns.observed_criterion_sigma_I 0.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 38.35 _reflns.d_resolution_high 2.20 _reflns.number_obs 9191 _reflns.number_all ? _reflns.percent_possible_obs 96.1 _reflns.pdbx_Rmerge_I_obs 0.03 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 16.80 _reflns.B_iso_Wilson_estimate 53.23 _reflns.pdbx_redundancy 3.9 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 2.20 _reflns_shell.d_res_low 2.32 _reflns_shell.percent_possible_all 98.2 _reflns_shell.Rmerge_I_obs 0.31 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.80 _reflns_shell.pdbx_redundancy 4.0 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3ZD4 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 9162 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.44 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 20.216 _refine.ls_d_res_high 2.200 _refine.ls_percent_reflns_obs 95.42 _refine.ls_R_factor_obs 0.1876 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1820 _refine.ls_R_factor_R_free 0.2360 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.9 _refine.ls_number_reflns_R_free 907 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model 'PDB ENTRY 2GOZ' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.33 _refine.pdbx_overall_phase_error 30.80 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1343 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 31 _refine_hist.number_atoms_total 1374 _refine_hist.d_res_high 2.200 _refine_hist.d_res_low 20.216 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function f_bond_d 0.005 ? ? 1500 'X-RAY DIFFRACTION' ? f_angle_d 0.938 ? ? 2331 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 14.735 ? ? 746 'X-RAY DIFFRACTION' ? f_chiral_restr 0.040 ? ? 311 'X-RAY DIFFRACTION' ? f_plane_restr 0.007 ? ? 63 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all 'X-RAY DIFFRACTION' . 2.2001 2.3377 1396 0.2845 98.00 0.3744 . . 160 . . 'X-RAY DIFFRACTION' . 2.3377 2.5179 1408 0.2933 98.00 0.3505 . . 152 . . 'X-RAY DIFFRACTION' . 2.5179 2.7707 1388 0.2840 98.00 0.3894 . . 157 . . 'X-RAY DIFFRACTION' . 2.7707 3.1703 1410 0.2330 97.00 0.3075 . . 151 . . 'X-RAY DIFFRACTION' . 3.1703 3.9892 1384 0.1487 96.00 0.1917 . . 148 . . 'X-RAY DIFFRACTION' . 3.9892 20.2172 1269 0.1283 86.00 0.1659 . . 139 . . # _database_PDB_matrix.entry_id 3ZD4 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 3ZD4 _struct.title 'Full-Length Hammerhead Ribozyme with G12A substitution at the general base position' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3ZD4 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, GENERAL BASE CATALYSIS' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 3ZD4 3ZD4 ? 1 ? 1 2 PDB 3ZD4 3ZD4 ? 2 ? 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3ZD4 A 1 ? 43 ? 3ZD4 1 ? 43 ? 1 43 2 2 3ZD4 B 1 ? 20 ? 3ZD4 1 ? 20 ? 1 20 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 3320 ? 1 MORE -7.2 ? 1 'SSA (A^2)' 10270 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A GDP 1 "O3'" ? ? ? 1_555 A G 2 P ? ? A GDP 1 A G 2 1_555 ? ? ? ? ? ? ? 1.594 ? ? covale2 covale both ? B U 5 "O3'" ? ? ? 1_555 B OMC 6 P ? ? B U 5 B OMC 6 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale3 covale both ? B OMC 6 "O3'" ? ? ? 1_555 B C 7 P ? ? B OMC 6 B C 7 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale4 covale both ? B C 19 "O3'" ? ? ? 1_555 B DC 20 P ? ? B C 19 B DC 20 1_555 ? ? ? ? ? ? ? 1.608 ? ? hydrog1 hydrog ? ? A GDP 1 N1 ? ? ? 1_555 B DC 20 N3 ? ? A GDP 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A GDP 1 N2 ? ? ? 1_555 B DC 20 O2 ? ? A GDP 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A GDP 1 O6 ? ? ? 1_555 B DC 20 N4 ? ? A GDP 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 19 N3 ? ? A G 2 B C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 19 O2 ? ? A G 2 B C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 19 N4 ? ? A G 2 B C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 B U 18 N3 ? ? A A 3 B U 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 B U 18 O4 ? ? A A 3 B U 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A U 4 O4 ? ? ? 1_555 B C 15 N4 ? ? A U 4 B C 15 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? hydrog10 hydrog ? ? A U 4 O2 ? ? ? 1_555 B A 17 N6 ? ? A U 4 B A 17 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog11 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 14 N3 ? ? A G 5 B C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 14 O2 ? ? A G 5 B C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 14 N4 ? ? A G 5 B C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 6 N3 ? ? ? 1_555 A A 28 N7 ? ? A U 6 A A 28 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog15 hydrog ? ? A U 6 O2 ? ? ? 1_555 A A 28 N6 ? ? A U 6 A A 28 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog16 hydrog ? ? A C 8 N4 ? ? ? 1_555 A C 26 O2 ? ? A C 8 A C 26 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog17 hydrog ? ? A C 8 O2 ? ? ? 1_555 A C 26 N4 ? ? A C 8 A C 26 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog18 hydrog ? ? A U 9 N3 ? ? ? 1_555 B A 12 N1 ? ? A U 9 B A 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 9 O4 ? ? ? 1_555 B A 12 N6 ? ? A U 9 B A 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 10 N1 ? ? ? 1_555 B U 11 N3 ? ? A A 10 B U 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 10 N6 ? ? ? 1_555 B U 11 O4 ? ? A A 10 B U 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 11 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 11 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 11 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 9 N1 ? ? A C 12 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 9 O6 ? ? A C 12 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 9 N2 ? ? A C 12 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A A 13 N1 ? ? ? 1_555 B U 8 N3 ? ? A A 13 B U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A A 13 N6 ? ? ? 1_555 B U 8 O4 ? ? A A 13 B U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 14 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 14 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 14 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 15 N3 ? ? ? 1_555 A G 20 N1 ? ? A C 15 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 15 N4 ? ? ? 1_555 A G 20 O6 ? ? A C 15 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 15 O2 ? ? ? 1_555 A G 20 N2 ? ? A C 15 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 17 N2 ? ? ? 1_555 A A 38 N1 ? ? A G 17 A A 38 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog37 hydrog ? ? A A 21 N6 ? ? ? 1_555 A A 36 N3 ? ? A A 21 A A 36 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog38 hydrog ? ? A G 22 N1 ? ? ? 1_555 A C 35 N3 ? ? A G 22 A C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A G 22 N2 ? ? ? 1_555 A C 35 O2 ? ? A G 22 A C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A G 22 O6 ? ? ? 1_555 A C 35 N4 ? ? A G 22 A C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A U 23 N3 ? ? ? 1_555 A A 34 N1 ? ? A U 23 A A 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A U 23 O4 ? ? ? 1_555 A A 34 N6 ? ? A U 23 A A 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A C 24 N3 ? ? ? 1_555 A G 33 N1 ? ? A C 24 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 24 N4 ? ? ? 1_555 A G 33 O6 ? ? A C 24 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 24 O2 ? ? ? 1_555 A G 33 N2 ? ? A C 24 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 25 N3 ? ? ? 1_555 A G 32 N1 ? ? A C 25 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 25 N4 ? ? ? 1_555 A G 32 O6 ? ? A C 25 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 25 O2 ? ? ? 1_555 A G 32 N2 ? ? A C 25 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A A 28 N3 ? ? ? 1_555 A U 30 N3 ? ? A A 28 A U 30 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog50 hydrog ? ? A A 31 N6 ? ? ? 1_555 B U 13 O2 ? ? A A 31 B U 13 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog51 hydrog ? ? A A 31 N7 ? ? ? 1_555 B U 13 N3 ? ? A A 31 B U 13 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog52 hydrog ? ? A A 37 N6 ? ? ? 1_555 B OMC 6 O2 ? ? A A 37 B OMC 6 1_555 ? ? ? ? ? ? 'A-OMC MISPAIR' ? ? ? hydrog53 hydrog ? ? A A 38 N6 ? ? ? 1_555 B OMC 6 O2 ? ? A A 38 B OMC 6 1_555 ? ? ? ? ? ? 'A-OMC MISPAIR' ? ? ? hydrog54 hydrog ? ? A A 39 N1 ? ? ? 1_555 B U 5 N3 ? ? A A 39 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A A 39 N6 ? ? ? 1_555 B U 5 O4 ? ? A A 39 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A C 40 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 40 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A C 40 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 40 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A C 40 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 40 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? A G 41 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 41 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? A G 41 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 41 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? A G 41 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 41 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? A C 42 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 42 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? A C 42 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 42 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? A C 42 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 42 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? A C 43 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 43 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? A C 43 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 43 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? A C 43 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 43 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 OP1 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 A _pdbx_validate_close_contact.auth_seq_id_1 29 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 2015 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.03 # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A GDP 1 A GDP 1 ? G "GUANOSINE-5'-DIPHOSPHATE" 2 B OMC 6 B OMC 6 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined -9.5342 18.6015 11.6618 0.5997 0.4442 0.3273 0.0597 -0.0497 0.0575 5.8229 2.1739 8.3154 1.9530 0.0423 -0.4410 0.3050 -0.1505 -0.3776 0.2587 -0.5892 -0.0871 1.4182 0.4680 0.3637 'X-RAY DIFFRACTION' 2 ? refined -11.2177 7.3014 -8.4746 0.3042 0.3588 0.4791 -0.0041 0.0582 -0.0199 0.5896 6.7655 1.4247 1.2146 0.9685 1.8026 -0.0108 -0.0107 -0.2627 -0.5724 0.2107 -0.9420 -0.1116 0.1653 -0.2598 'X-RAY DIFFRACTION' 3 ? refined -17.7545 10.0028 -21.1917 0.5547 0.4813 0.4111 -0.1595 0.0215 0.0566 3.3811 5.2670 4.1046 0.4805 2.6882 3.6670 -0.6330 0.4047 0.2650 -0.7350 0.8563 -0.1389 -0.9638 0.5514 -0.2880 'X-RAY DIFFRACTION' 4 ? refined -18.2220 15.6795 0.3312 0.4933 0.7181 0.5702 0.0280 -0.0638 -0.1811 9.4704 8.7572 8.6600 -2.7584 -3.9634 -0.2352 -1.1293 -1.7006 0.3625 1.0332 -0.0925 0.6589 -0.2176 -0.9127 1.1960 'X-RAY DIFFRACTION' 5 ? refined -22.8271 14.1219 -9.8188 0.4401 0.6258 0.4785 0.1070 -0.1613 -0.0808 7.1890 8.6537 8.0079 -3.6808 4.4502 -1.6796 0.0083 -0.3993 0.2379 -0.3373 -0.1489 0.5823 -0.5728 -1.6194 0.1746 'X-RAY DIFFRACTION' 6 ? refined -23.5303 17.2769 -24.8286 1.1338 0.9593 0.6167 0.2002 -0.3708 -0.0864 5.2889 5.8918 0.3828 3.6852 -1.4027 -1.1376 -1.4455 0.0748 1.0929 -0.5302 0.1727 -0.3188 -2.2335 -1.9499 1.0524 'X-RAY DIFFRACTION' 7 ? refined -31.3871 7.4091 -32.9070 0.6271 0.4999 0.3101 0.0140 0.0163 0.0282 2.9146 5.7936 5.4784 -2.6952 2.9942 -1.3478 0.3934 -0.0758 -0.0892 -0.5746 -0.2651 -0.0807 -0.7925 -0.0265 -0.1376 'X-RAY DIFFRACTION' 8 ? refined -30.4950 12.5137 -25.5497 0.6249 0.7158 0.3262 -0.0341 -0.0238 0.1084 3.9599 1.0698 2.1025 -1.3778 2.3283 -0.1344 -0.0626 -0.6905 -0.0826 0.2810 -0.0560 -0.0049 -0.3903 -0.6468 0.1255 'X-RAY DIFFRACTION' 9 ? refined -14.8169 2.4452 -3.7866 0.4593 0.4172 0.4521 -0.0898 -0.0010 0.0825 0.0526 5.1893 3.0583 -0.3828 -0.4311 1.5050 0.2296 -0.3693 -0.2889 0.7241 -0.2185 -0.6208 0.7800 -0.6640 -0.0468 'X-RAY DIFFRACTION' 10 ? refined -0.3432 22.0699 9.4899 0.3464 0.3638 0.4943 0.0749 -0.0350 0.0217 6.4416 4.0500 9.8534 2.3463 0.8041 0.8010 0.6212 -0.3305 -0.7250 -0.1020 -0.0247 -0.6883 -0.2298 -0.3106 -0.5422 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 1:4)' 'X-RAY DIFFRACTION' 2 2 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 5:14)' 'X-RAY DIFFRACTION' 3 3 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 15:25)' 'X-RAY DIFFRACTION' 4 4 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 26:30)' 'X-RAY DIFFRACTION' 5 5 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 31:34)' 'X-RAY DIFFRACTION' 6 6 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 35:38)' 'X-RAY DIFFRACTION' 7 7 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 39:43)' 'X-RAY DIFFRACTION' 8 8 ? ? ? ? ? ? ? ? ? '(CHAIN B AND RESID 1:7)' 'X-RAY DIFFRACTION' 9 9 ? ? ? ? ? ? ? ? ? '(CHAIN B AND RESID 8:15)' 'X-RAY DIFFRACTION' 10 10 ? ? ? ? ? ? ? ? ? '(CHAIN B AND RESID 16:20)' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 DC OP3 O N N 73 DC P P N N 74 DC OP1 O N N 75 DC OP2 O N N 76 DC "O5'" O N N 77 DC "C5'" C N N 78 DC "C4'" C N R 79 DC "O4'" O N N 80 DC "C3'" C N S 81 DC "O3'" O N N 82 DC "C2'" C N N 83 DC "C1'" C N R 84 DC N1 N N N 85 DC C2 C N N 86 DC O2 O N N 87 DC N3 N N N 88 DC C4 C N N 89 DC N4 N N N 90 DC C5 C N N 91 DC C6 C N N 92 DC HOP3 H N N 93 DC HOP2 H N N 94 DC "H5'" H N N 95 DC "H5''" H N N 96 DC "H4'" H N N 97 DC "H3'" H N N 98 DC "HO3'" H N N 99 DC "H2'" H N N 100 DC "H2''" H N N 101 DC "H1'" H N N 102 DC H41 H N N 103 DC H42 H N N 104 DC H5 H N N 105 DC H6 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 GDP PB P N N 145 GDP O1B O N N 146 GDP O2B O N N 147 GDP O3B O N N 148 GDP O3A O N N 149 GDP PA P N N 150 GDP O1A O N N 151 GDP O2A O N N 152 GDP "O5'" O N N 153 GDP "C5'" C N N 154 GDP "C4'" C N R 155 GDP "O4'" O N N 156 GDP "C3'" C N S 157 GDP "O3'" O N N 158 GDP "C2'" C N R 159 GDP "O2'" O N N 160 GDP "C1'" C N R 161 GDP N9 N Y N 162 GDP C8 C Y N 163 GDP N7 N Y N 164 GDP C5 C Y N 165 GDP C6 C N N 166 GDP O6 O N N 167 GDP N1 N N N 168 GDP C2 C N N 169 GDP N2 N N N 170 GDP N3 N N N 171 GDP C4 C Y N 172 GDP HOB2 H N N 173 GDP HOB3 H N N 174 GDP HOA2 H N N 175 GDP "H5'" H N N 176 GDP "H5''" H N N 177 GDP "H4'" H N N 178 GDP "H3'" H N N 179 GDP "HO3'" H N N 180 GDP "H2'" H N N 181 GDP "HO2'" H N N 182 GDP "H1'" H N N 183 GDP H8 H N N 184 GDP HN1 H N N 185 GDP HN21 H N N 186 GDP HN22 H N N 187 HOH O O N N 188 HOH H1 H N N 189 HOH H2 H N N 190 OMC N1 N N N 191 OMC C2 C N N 192 OMC N3 N N N 193 OMC C4 C N N 194 OMC C5 C N N 195 OMC C6 C N N 196 OMC O2 O N N 197 OMC N4 N N N 198 OMC "C1'" C N R 199 OMC "C2'" C N R 200 OMC "O2'" O N N 201 OMC CM2 C N N 202 OMC "C3'" C N R 203 OMC "C4'" C N R 204 OMC "O4'" O N N 205 OMC "O3'" O N N 206 OMC "C5'" C N N 207 OMC "O5'" O N N 208 OMC P P N N 209 OMC OP1 O N N 210 OMC OP2 O N N 211 OMC OP3 O N N 212 OMC H5 H N N 213 OMC H6 H N N 214 OMC HN41 H N N 215 OMC HN42 H N N 216 OMC "H1'" H N N 217 OMC "H2'" H N N 218 OMC HM21 H N N 219 OMC HM22 H N N 220 OMC HM23 H N N 221 OMC "H3'" H N N 222 OMC "H4'" H N N 223 OMC "HO3'" H N N 224 OMC "H5'" H N N 225 OMC "H5''" H N N 226 OMC HOP2 H N N 227 OMC HOP3 H N N 228 U OP3 O N N 229 U P P N N 230 U OP1 O N N 231 U OP2 O N N 232 U "O5'" O N N 233 U "C5'" C N N 234 U "C4'" C N R 235 U "O4'" O N N 236 U "C3'" C N S 237 U "O3'" O N N 238 U "C2'" C N R 239 U "O2'" O N N 240 U "C1'" C N R 241 U N1 N N N 242 U C2 C N N 243 U O2 O N N 244 U N3 N N N 245 U C4 C N N 246 U O4 O N N 247 U C5 C N N 248 U C6 C N N 249 U HOP3 H N N 250 U HOP2 H N N 251 U "H5'" H N N 252 U "H5''" H N N 253 U "H4'" H N N 254 U "H3'" H N N 255 U "HO3'" H N N 256 U "H2'" H N N 257 U "HO2'" H N N 258 U "H1'" H N N 259 U H3 H N N 260 U H5 H N N 261 U H6 H N N 262 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 DC OP3 P sing N N 76 DC OP3 HOP3 sing N N 77 DC P OP1 doub N N 78 DC P OP2 sing N N 79 DC P "O5'" sing N N 80 DC OP2 HOP2 sing N N 81 DC "O5'" "C5'" sing N N 82 DC "C5'" "C4'" sing N N 83 DC "C5'" "H5'" sing N N 84 DC "C5'" "H5''" sing N N 85 DC "C4'" "O4'" sing N N 86 DC "C4'" "C3'" sing N N 87 DC "C4'" "H4'" sing N N 88 DC "O4'" "C1'" sing N N 89 DC "C3'" "O3'" sing N N 90 DC "C3'" "C2'" sing N N 91 DC "C3'" "H3'" sing N N 92 DC "O3'" "HO3'" sing N N 93 DC "C2'" "C1'" sing N N 94 DC "C2'" "H2'" sing N N 95 DC "C2'" "H2''" sing N N 96 DC "C1'" N1 sing N N 97 DC "C1'" "H1'" sing N N 98 DC N1 C2 sing N N 99 DC N1 C6 sing N N 100 DC C2 O2 doub N N 101 DC C2 N3 sing N N 102 DC N3 C4 doub N N 103 DC C4 N4 sing N N 104 DC C4 C5 sing N N 105 DC N4 H41 sing N N 106 DC N4 H42 sing N N 107 DC C5 C6 doub N N 108 DC C5 H5 sing N N 109 DC C6 H6 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 GDP PB O1B doub N N 151 GDP PB O2B sing N N 152 GDP PB O3B sing N N 153 GDP PB O3A sing N N 154 GDP O2B HOB2 sing N N 155 GDP O3B HOB3 sing N N 156 GDP O3A PA sing N N 157 GDP PA O1A doub N N 158 GDP PA O2A sing N N 159 GDP PA "O5'" sing N N 160 GDP O2A HOA2 sing N N 161 GDP "O5'" "C5'" sing N N 162 GDP "C5'" "C4'" sing N N 163 GDP "C5'" "H5'" sing N N 164 GDP "C5'" "H5''" sing N N 165 GDP "C4'" "O4'" sing N N 166 GDP "C4'" "C3'" sing N N 167 GDP "C4'" "H4'" sing N N 168 GDP "O4'" "C1'" sing N N 169 GDP "C3'" "O3'" sing N N 170 GDP "C3'" "C2'" sing N N 171 GDP "C3'" "H3'" sing N N 172 GDP "O3'" "HO3'" sing N N 173 GDP "C2'" "O2'" sing N N 174 GDP "C2'" "C1'" sing N N 175 GDP "C2'" "H2'" sing N N 176 GDP "O2'" "HO2'" sing N N 177 GDP "C1'" N9 sing N N 178 GDP "C1'" "H1'" sing N N 179 GDP N9 C8 sing Y N 180 GDP N9 C4 sing Y N 181 GDP C8 N7 doub Y N 182 GDP C8 H8 sing N N 183 GDP N7 C5 sing Y N 184 GDP C5 C6 sing N N 185 GDP C5 C4 doub Y N 186 GDP C6 O6 doub N N 187 GDP C6 N1 sing N N 188 GDP N1 C2 sing N N 189 GDP N1 HN1 sing N N 190 GDP C2 N2 sing N N 191 GDP C2 N3 doub N N 192 GDP N2 HN21 sing N N 193 GDP N2 HN22 sing N N 194 GDP N3 C4 sing N N 195 HOH O H1 sing N N 196 HOH O H2 sing N N 197 OMC N1 C2 sing N N 198 OMC N1 C6 sing N N 199 OMC N1 "C1'" sing N N 200 OMC C2 N3 sing N N 201 OMC C2 O2 doub N N 202 OMC N3 C4 doub N N 203 OMC C4 C5 sing N N 204 OMC C4 N4 sing N N 205 OMC C5 C6 doub N N 206 OMC C5 H5 sing N N 207 OMC C6 H6 sing N N 208 OMC N4 HN41 sing N N 209 OMC N4 HN42 sing N N 210 OMC "C1'" "C2'" sing N N 211 OMC "C1'" "O4'" sing N N 212 OMC "C1'" "H1'" sing N N 213 OMC "C2'" "O2'" sing N N 214 OMC "C2'" "C3'" sing N N 215 OMC "C2'" "H2'" sing N N 216 OMC "O2'" CM2 sing N N 217 OMC CM2 HM21 sing N N 218 OMC CM2 HM22 sing N N 219 OMC CM2 HM23 sing N N 220 OMC "C3'" "C4'" sing N N 221 OMC "C3'" "O3'" sing N N 222 OMC "C3'" "H3'" sing N N 223 OMC "C4'" "O4'" sing N N 224 OMC "C4'" "C5'" sing N N 225 OMC "C4'" "H4'" sing N N 226 OMC "O3'" "HO3'" sing N N 227 OMC "C5'" "O5'" sing N N 228 OMC "C5'" "H5'" sing N N 229 OMC "C5'" "H5''" sing N N 230 OMC "O5'" P sing N N 231 OMC P OP1 doub N N 232 OMC P OP2 sing N N 233 OMC P OP3 sing N N 234 OMC OP2 HOP2 sing N N 235 OMC OP3 HOP3 sing N N 236 U OP3 P sing N N 237 U OP3 HOP3 sing N N 238 U P OP1 doub N N 239 U P OP2 sing N N 240 U P "O5'" sing N N 241 U OP2 HOP2 sing N N 242 U "O5'" "C5'" sing N N 243 U "C5'" "C4'" sing N N 244 U "C5'" "H5'" sing N N 245 U "C5'" "H5''" sing N N 246 U "C4'" "O4'" sing N N 247 U "C4'" "C3'" sing N N 248 U "C4'" "H4'" sing N N 249 U "O4'" "C1'" sing N N 250 U "C3'" "O3'" sing N N 251 U "C3'" "C2'" sing N N 252 U "C3'" "H3'" sing N N 253 U "O3'" "HO3'" sing N N 254 U "C2'" "O2'" sing N N 255 U "C2'" "C1'" sing N N 256 U "C2'" "H2'" sing N N 257 U "O2'" "HO2'" sing N N 258 U "C1'" N1 sing N N 259 U "C1'" "H1'" sing N N 260 U N1 C2 sing N N 261 U N1 C6 sing N N 262 U C2 O2 doub N N 263 U C2 N3 sing N N 264 U N3 C4 sing N N 265 U N3 H3 sing N N 266 U C4 O4 doub N N 267 U C4 C5 sing N N 268 U C5 C6 doub N N 269 U C5 H5 sing N N 270 U C6 H6 sing N N 271 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3ZD4 'double helix' 3ZD4 'a-form double helix' 3ZD4 'hairpin loop' 3ZD4 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A GDP 1 1_555 B DC 20 1_555 -0.706 -0.181 -0.057 -6.475 -3.555 5.134 1 A_GDP1:DC20_B A 1 ? B 20 ? 19 1 1 A G 2 1_555 B C 19 1_555 -0.502 -0.258 -0.291 -10.413 -9.392 1.604 2 A_G2:C19_B A 2 ? B 19 ? 19 1 1 A A 3 1_555 B U 18 1_555 0.128 -0.152 0.092 -7.328 -7.186 1.491 3 A_A3:U18_B A 3 ? B 18 ? 20 1 1 A U 4 1_555 B C 15 1_555 -1.071 -0.017 -0.880 -4.307 -5.425 -34.434 4 A_U4:C15_B A 4 ? B 15 ? ? ? 1 A G 5 1_555 B C 14 1_555 -0.218 -0.145 0.398 0.587 -14.824 -0.212 5 A_G5:C14_B A 5 ? B 14 ? 19 1 1 A U 6 1_555 A A 28 1_555 4.045 -2.263 -0.438 -12.525 -5.701 -94.910 6 A_U6:A28_A A 6 ? A 28 ? 24 4 1 A A 31 1_555 B U 13 1_555 -4.098 -2.150 -0.598 -12.123 -0.153 -94.586 7 A_A31:U13_B A 31 ? B 13 ? 24 4 1 A U 9 1_555 B A 12 1_555 -0.219 -0.088 0.598 7.568 -9.175 4.412 8 A_U9:A12_B A 9 ? B 12 ? 20 1 1 A A 10 1_555 B U 11 1_555 -0.009 -0.067 0.158 16.077 -16.561 6.065 9 A_A10:U11_B A 10 ? B 11 ? 20 1 1 A C 11 1_555 B G 10 1_555 0.434 -0.208 0.035 7.468 -20.708 4.938 10 A_C11:G10_B A 11 ? B 10 ? 19 1 1 A C 12 1_555 B G 9 1_555 0.078 -0.144 0.253 -5.529 -9.579 4.010 11 A_C12:G9_B A 12 ? B 9 ? 19 1 1 A A 13 1_555 B U 8 1_555 0.147 -0.217 -0.016 -7.696 -12.764 2.084 12 A_A13:U8_B A 13 ? B 8 ? 20 1 1 A G 14 1_555 B C 7 1_555 0.060 -0.148 0.475 4.165 -16.341 0.281 13 A_G14:C7_B A 14 ? B 7 ? 19 1 1 A C 15 1_555 A G 20 1_555 0.361 -0.197 -0.492 10.147 1.399 -2.747 14 A_C15:G20_A A 15 ? A 20 ? 19 1 1 A C 8 1_555 A C 26 1_555 1.949 1.895 -0.211 11.301 5.773 179.121 15 A_C8:C26_A A 8 ? A 26 ? 15 2 1 A G 32 1_555 A C 25 1_555 -0.259 -0.153 0.208 -0.336 -6.680 0.271 16 A_G32:C25_A A 32 ? A 25 ? 19 1 1 A G 33 1_555 A C 24 1_555 -0.536 -0.122 0.101 -6.564 -13.656 5.620 17 A_G33:C24_A A 33 ? A 24 ? 19 1 1 A A 34 1_555 A U 23 1_555 0.010 -0.191 -0.075 -6.196 -10.360 -0.211 18 A_A34:U23_A A 34 ? A 23 ? 20 1 1 A C 35 1_555 A G 22 1_555 0.240 -0.215 0.556 -5.279 -4.847 0.239 19 A_C35:G22_A A 35 ? A 22 ? 19 1 1 A A 36 1_555 A A 21 1_555 6.430 -3.797 0.508 -2.557 -13.939 -18.004 20 A_A36:A21_A A 36 ? A 21 ? ? 10 1 A A 37 1_555 B OMC 6 1_555 -6.116 -2.852 -1.615 -20.898 -13.423 -37.287 21 A_A37:OMC6_B A 37 ? B 6 ? ? ? 1 A A 38 1_555 A G 17 1_555 -3.879 3.475 0.231 29.841 -44.817 83.249 22 A_A38:G17_A A 38 ? A 17 ? ? ? 1 A A 39 1_555 B U 5 1_555 -0.383 0.025 0.440 -0.049 -3.112 3.155 23 A_A39:U5_B A 39 ? B 5 ? 20 1 1 A C 40 1_555 B G 4 1_555 0.298 -0.236 0.136 5.528 -15.948 1.137 24 A_C40:G4_B A 40 ? B 4 ? 19 1 1 A G 41 1_555 B C 3 1_555 -0.624 -0.252 0.094 -2.075 -17.244 0.464 25 A_G41:C3_B A 41 ? B 3 ? 19 1 1 A C 42 1_555 B G 2 1_555 0.045 -0.231 0.332 -6.142 -13.639 0.724 26 A_C42:G2_B A 42 ? B 2 ? 19 1 1 A C 43 1_555 B G 1 1_555 0.564 -0.360 0.091 4.489 -3.015 -1.973 27 A_C43:G1_B A 43 ? B 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A GDP 1 1_555 B DC 20 1_555 A G 2 1_555 B C 19 1_555 -0.268 -2.142 3.477 1.284 2.974 30.286 -4.690 0.774 3.243 5.671 -2.449 30.455 1 AA_GDP1G2:C19DC20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A G 2 1_555 B C 19 1_555 A A 3 1_555 B U 18 1_555 -0.135 -1.444 3.188 -0.984 5.610 35.758 -3.067 0.087 2.938 9.066 1.591 36.195 2 AA_G2A3:U18C19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A A 3 1_555 B U 18 1_555 A U 4 1_555 B C 15 1_555 3.174 -1.271 4.213 -5.896 10.016 66.337 -1.625 -3.148 3.749 9.081 5.345 67.233 3 AA_A3U4:C15U18_BB A 3 ? B 18 ? A 4 ? B 15 ? 1 A U 4 1_555 B C 15 1_555 A G 5 1_555 B C 14 1_555 1.766 -1.675 3.187 -11.440 11.030 33.078 -3.902 -4.093 1.863 18.129 18.802 36.600 4 AA_U4G5:C14C15_BB A 4 ? B 15 ? A 5 ? B 14 ? 1 A G 5 1_555 B C 14 1_555 A U 6 1_555 A A 28 1_555 -2.690 -1.998 3.524 4.165 -2.160 83.378 -1.445 2.127 3.453 -1.623 -3.129 83.486 5 AA_G5U6:A28C14_AB A 5 ? B 14 ? A 6 ? A 28 ? 1 A U 6 1_555 A A 28 1_555 A A 31 1_555 B U 13 1_555 3.272 -3.467 5.282 40.992 -68.809 -150.465 2.126 1.881 4.430 35.221 20.983 -157.496 6 AA_U6A31:U13A28_BA A 6 ? A 28 ? A 31 ? B 13 ? 1 A A 31 1_555 B U 13 1_555 A U 9 1_555 B A 12 1_555 1.563 -1.233 2.861 -15.049 2.723 76.148 -1.050 -1.607 2.526 2.187 12.086 77.439 7 AA_A31U9:A12U13_BB A 31 ? B 13 ? A 9 ? B 12 ? 1 A U 9 1_555 B A 12 1_555 A A 10 1_555 B U 11 1_555 -0.384 -1.349 2.791 1.077 11.909 32.616 -3.694 0.773 2.167 20.371 -1.842 34.683 8 AA_U9A10:U11A12_BB A 9 ? B 12 ? A 10 ? B 11 ? 1 A A 10 1_555 B U 11 1_555 A C 11 1_555 B G 10 1_555 0.317 -1.376 3.452 0.991 6.077 36.008 -3.055 -0.366 3.193 9.742 -1.588 36.513 9 AA_A10C11:G10U11_BB A 10 ? B 11 ? A 11 ? B 10 ? 1 A C 11 1_555 B G 10 1_555 A C 12 1_555 B G 9 1_555 -0.912 -2.197 3.407 -4.128 11.705 28.101 -6.304 0.965 2.427 22.753 8.025 30.670 10 AA_C11C12:G9G10_BB A 11 ? B 10 ? A 12 ? B 9 ? 1 A C 12 1_555 B G 9 1_555 A A 13 1_555 B U 8 1_555 -0.055 -1.024 3.072 3.518 18.790 35.599 -3.341 0.427 2.261 28.355 -5.309 40.260 11 AA_C12A13:U8G9_BB A 12 ? B 9 ? A 13 ? B 8 ? 1 A A 13 1_555 B U 8 1_555 A G 14 1_555 B C 7 1_555 0.802 -1.447 2.919 1.174 7.675 26.158 -4.672 -1.455 2.436 16.501 -2.523 27.267 12 AA_A13G14:C7U8_BB A 13 ? B 8 ? A 14 ? B 7 ? 1 A G 14 1_555 B C 7 1_555 A C 15 1_555 A G 20 1_555 0.304 0.217 3.288 12.046 5.664 36.818 -0.376 1.036 3.226 8.628 -18.352 39.072 13 AA_G14C15:G20C7_AB A 14 ? B 7 ? A 15 ? A 20 ? 1 A C 8 1_555 A C 26 1_555 A G 32 1_555 A C 25 1_555 -2.442 -2.108 1.189 87.002 -154.566 125.925 -0.788 1.371 1.349 -77.408 -43.571 178.804 14 AA_C8G32:C25C26_AA A 8 ? A 26 ? A 32 ? A 25 ? 1 A G 32 1_555 A C 25 1_555 A G 33 1_555 A C 24 1_555 0.736 -1.877 3.258 4.056 6.279 31.480 -4.432 -0.636 2.909 11.373 -7.347 32.334 15 AA_G32G33:C24C25_AA A 32 ? A 25 ? A 33 ? A 24 ? 1 A G 33 1_555 A C 24 1_555 A A 34 1_555 A U 23 1_555 -0.773 -1.546 3.147 -0.013 6.733 35.917 -3.323 1.232 2.821 10.801 0.021 36.522 16 AA_G33A34:U23C24_AA A 33 ? A 24 ? A 34 ? A 23 ? 1 A A 34 1_555 A U 23 1_555 A C 35 1_555 A G 22 1_555 0.415 -1.331 3.198 -3.166 8.622 31.708 -3.694 -1.227 2.701 15.380 5.649 32.979 17 AA_A34C35:G22U23_AA A 34 ? A 23 ? A 35 ? A 22 ? 1 A C 35 1_555 A G 22 1_555 A A 36 1_555 A A 21 1_555 0.252 -1.344 3.287 5.282 4.608 55.970 -1.681 0.029 3.186 4.889 -5.604 56.372 18 AA_C35A36:A21G22_AA A 35 ? A 22 ? A 36 ? A 21 ? 1 A A 36 1_555 A A 21 1_555 A A 37 1_555 B OMC 6 1_555 1.406 -1.758 4.069 12.846 5.837 23.552 -5.581 1.149 3.787 12.921 -28.435 27.404 19 AA_A36A37:OMC6A21_BA A 36 ? A 21 ? A 37 ? B 6 ? 1 A A 37 1_555 B OMC 6 1_555 A A 38 1_555 A G 17 1_555 0.201 -3.957 1.858 -27.072 31.941 -20.016 1.717 -2.562 3.646 -50.020 -42.396 -46.214 20 AA_A37A38:G17OMC6_AB A 37 ? B 6 ? A 38 ? A 17 ? 1 A A 38 1_555 A G 17 1_555 A A 39 1_555 B U 5 1_555 0.803 2.523 3.423 -3.045 -18.766 84.632 2.254 -0.653 2.900 -13.787 2.237 86.346 21 AA_A38A39:U5G17_BA A 38 ? A 17 ? A 39 ? B 5 ? 1 A A 39 1_555 B U 5 1_555 A C 40 1_555 B G 4 1_555 -0.261 -1.098 3.198 1.447 9.545 32.666 -3.294 0.661 2.763 16.526 -2.505 34.025 22 AA_A39C40:G4U5_BB A 39 ? B 5 ? A 40 ? B 4 ? 1 A C 40 1_555 B G 4 1_555 A G 41 1_555 B C 3 1_555 -0.031 -1.580 3.307 -0.509 12.331 30.673 -4.712 -0.026 2.503 22.216 0.917 33.008 23 AA_C40G41:C3G4_BB A 40 ? B 4 ? A 41 ? B 3 ? 1 A G 41 1_555 B C 3 1_555 A C 42 1_555 B G 2 1_555 0.323 -1.289 3.301 0.733 10.667 37.227 -3.203 -0.401 2.844 16.302 -1.121 38.680 24 AA_G41C42:G2C3_BB A 41 ? B 3 ? A 42 ? B 2 ? 1 A C 42 1_555 B G 2 1_555 A C 43 1_555 B G 1 1_555 1.169 -2.188 2.958 5.907 5.269 26.975 -5.598 -1.185 2.681 10.998 -12.331 28.091 25 AA_C42C43:G1G2_BB A 42 ? B 2 ? A 43 ? B 1 ? # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 2GOZ _pdbx_initial_refinement_model.details 'PDB ENTRY 2GOZ' # _atom_sites.entry_id 3ZD4 _atom_sites.fract_transf_matrix[1][1] 0.019944 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.008286 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.014609 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.017982 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_